[{"id":1,"field":"some value to keep"},{"id":2,"field":"some value to keep"}]

db.aggregate([{"$documents":[//yourpythondicthere{"id":1,"from_value_key":"x"},{"id":2,"from_value_key":"y"},{"id":4,"from_value_key":"z"}]},{"$merge":{"into":"collection","on":"id","whenMatched":"merge"}}])